Ultra-thin composite carbon molecular sieve (CMS) membranes were fabricated on well-defined inorganic alumina substrates using a polymer of intrinsic microporosity (PIM) polyimide as precursor. Details of the pyrolysis-related structural development were elucidated using focused-beam, interference-enhanced spectroscopic ellipsometry (both in the UV-VIS and IR range) which allowed accurate determination of the film thickness, optical properties as well as following the chemical transformations. The pyrolysis-induced collapse of thin and bulk PIM-derived CMS membranes was compared with CMS made from a well-known non-PIM precursor 6FDA-DABA. Significant differences between the PIM and non-PIM precursors were discovered and explained by a much larger possible volume contraction in the PIM. In spite of the differences, surprisingly, the gas separation properties did not fundamentally differ. The high temperature collapse of the initially amorphous and isotropic precursor structure was accompanied by a significant molecular orientation within the formed turbostratic carbon network guided by the laterally constraining presence of the substrate. This manifested itself in the development of uniaxial optical anisotropy, which was shown to correlate with increases in gas separation selectivity for multiple technologically important gas pairs. Reduction of CMS skin thickness significantly below ~1 micron induced large losses in permeability coefficients with only small to moderate effects on selectivity. Remarkably, skin thickness reduction and physical aging seemed to superimpose onto the same trend, which explains and strengthens some of the earlier fundamental insights.